The Devil and the Deep Blue Sea
by Wormhole
Summary: Sequel to What Lies Beneath - Something sinister lurks in the ocean. Now Beta'd.
1. Chapter 1: Light's Out

Notes and Credits

**Notes**: This story takes place after - What Lies Beneath (please see profile)

**Beta Reader:** Sparklyshimmer2010

**The Devil and The Deep Blue Sea**

**Chapter One: - Light's Out**

Elizabeth was sitting in her office when it happened. Reports were coming in from all over the city. Lights were systematically turning off and emergency lighting was coming on. It wasn't long before she and the other people in the Control Tower fell victim to the problem plaguing them.

--

Rodney was already on the case. He had picked a team of skilful scientists, Radek being one of them, and together with a handful of flashlights they tried to find the source of the problem.

They started by visiting the first reported incident and that location was in the lower part of the city. A team had been working in that area for about a year and were restoring some of the functions in the rooms they had found.

The emergency lighting was barely efficient enough to work in, so in one room the restoration team had been sitting idol waiting for a repair crew to arrive having been ordered not to touch anything and to stay put. When they saw Rodney and his team, the four of them quickly scrambled to their feet, bringing the number of people in the room to eight.

Rodney shone his flashlight at each person individually before he picked someone out at random and pretending to know his name he started to question him. "Just the person, I need you to explain to me exactly what happened here before the lights went out."

Dumfounded by the unexpected approach from his superior, the tall dark haired scientist explained what had happened. "Not much to explain, Adams was assigned to work on the panel over there then the lights suddenly went out."

Rodney followed the direction the man had pointed to and his eyes fell on the control panel at the back of the room. "What was the last control switch touched?"

Everyone turned to face Adams. "I swear the lights went out before I touched anything."

Rodney sighed; it was going to be one of those days.

--

John entered Elizabeth's office only to find her pacing the room. "Problems?"

Elizabeth spun round at the sound of John's voice and saw him standing in front of her desk. "So it would seem." Pulling her chair out she sat back down. "Rodney is investigating the situation but so far he hasn't a clue to the power loss."

"How many people does it take to fix a light bulb?" asked John sarcastically, in an attempt to get one up on Rodney.

Elizabeth half smiled at the attempted humour in John's voice. "Not enough it would seem."

Elizabeth noticed Chuck appear in the doorway. "Ma'am sorry to disturb you but the sensors have picked up an anonymous reading on the ocean bed."

Raising a curious eyebrow at John whilst getting up from her chair, they both followed Chuck.

--

In the Control Room by the monitor screen, Chuck pointed out what appeared to be something large moving in the water near the edge of the city. "It appeared a few minutes ago."

"No indications as to what it is?" asked Elizabeth.

John remembered his encounter with the whales when they rescued Rodney from a downed Puddle Jumper. "Not one of the whales we discovered a few months back is it?"

Chuck shook his head. " Too small for that. We're not even sure if it's a life sign."

This got John curious; normally the sensors would indicate if that were so. "What else could it be?"

--

John had taken a Puddle Jumper out and flown it into the ocean to search for the illusive object the cities sensors had detected. Doctor Weir's voice came over the ships intercom system. "Anything John?"

Keeping a lookout on the forward porthole John responded to her call. "Nothing yet. I'm not picking up anything on these sensors."

The connection cut out for a second before Elizabeth responded. "We're picking it up on the other side of the city. Opposite to where you are."

"Copy that." John turned the Puddle Jumper full circle to see if he could spot it. "I can't see it, I'm going to fly under the city rather then around."

"Understood. Be careful."

Proceeding as reported John took the Puddle Jumper underneath and across to the other side. Halfway he contacted the Control Tower. "Am I getting close?"

John could hear the tension in Elizabeth's voice, as he supposedly got closer to the object. "Not far. Just a few minutes from your current position."

Even with the headlights on, it was still too dark to see in the waters clearly. "I can't see a thing."

"_Your almost on top of it Sir_," came Chuck's voice.

Suddenly the whole console exploded as lightning engulfed the ship and John blacked out on contact with it.

**TBC**


	2. Chapter 2: The Chase

**Chapter Two:- The Chase**

John woke to the familiar sound of monitors beeping next to him and knew straight away he was in the infirmary on Atlantis. He opened his eyes, only to find his vision was all blurred. It took a moment for them to adjust and saw the good doctor looking down at him with a smile on his face.

He turned when he felt a light, comforting touch on his left shoulder and saw Elizabeth standing there and wished he had looked in that direction first.

"How are you feeling?"

John turned back at the sound of Carson's voice and shifted a bit to make himself more comfortable. That in turn answered the question as he winced a bit from the movement. "Sore."

"John." John turned back to face Elizabeth. "Can you tell us what happened? What did you see?"

He shook his head solemnly. "I didn't see it. But I can guess what it was. There's only one creature I know that can produce and electrified field like the one which knocked out the Puddle Jumper."

Elizabeth waited for an answer.

"At a guess, I say our snake friends are back."

"But we got rid of them."

John raised a hand painfully to correct her. "Correction, we got rid of one and her babies. I'd say Daddy has decided to come out and play. Also I don't think he's as friendly as the first was and that's an understatement."

"All I can say is," interrupted Carson, "you're lucky the Puddle Jumper took the full force of the field. Had it been you the creature struck -if it was the creature- you certainly would've been killed."

"Just as well I didn't take my favourite Puddle Jumper then." Joked John and he couldn't help but snigger a bit. "How did you guys get me out anyway?"

"I see you haven't lost your sense of humour then," teased Carson as he checked his chart he retrieved from the end of the bed and let Elizabeth answer his question.

"You have Rodney to thank for that. He used the same technique your team used to rescue him from a downed Puddle Jumper."

John smiled at the news before Carson intervened again. "I think we need to let our patient have his rest and you too Elizabeth. You've been up for the past twenty four hours."

John looked from Carson to Elizabeth. "Twenty four hours and no sign of the creature since then?"

Elizabeth nodded. "Yes and no. It hasn't reappeared on our scanners yet."

"Has Rodney had any luck with the lights?"

"No. He's still working on that. Anyway I best leave you to it and get some rest of my own."

"I'm sure he'll get them fixed!" shouted out John as Elizabeth was by the doorway. She turned back round and showed a bit of encouragement on her face before leaving.

--

It was well into the early hours of the morning and Elizabeth was just on her way back to her quarters to catch a few hours sleep, when she spotted the snake in the corridor blocking her path. She was surprised it was even in the city and she hadn't been alerted of its presence.

It hadn't seen her yet as it was looking into an empty room, its tail just visible, so she slowly and carefully moved backwards out of sight towards the nearest corner, which was three rooms away. She had just about reached the last room when her earpiece activated and she cringed at the noise.

The snake had heard it. Its head immediately withdrew out the room and it locked eyes on her almost immediately as whoever contacted her started to speak. "_Dr. Weir, we're picking up the snake in your area_. _Advise you leave immediately_."

Elizabeth slowly reached for her headset and pressed it to respond. "Yes Radek I'm

well aware of that. It's looking straight at me."

"_We only just picked it up, something is interfering with sensors. Personnel have been notified to stay in their room. Move into the adjoining corridor and we'll seal that section off. A security team is on the way."_

Elizabeth looked round the corner to see how far the dividing section was. It was a good distance away. The snake had already started moving towards her. She wasted no time following Radek's suggestion. "Just leave it open for me." With that she turned and ran.

The snake instantly gave chase and was closing fast.

Looking round she doubled her speed when she saw how close it was and re-established connection with Radek. "I'm almost there, get ready to hit that…."

--

Radek was in the control room and looked and Rodney who was working on another system when they heard her scream. Suggest

**TBC**


	3. Chapter 3: Venom

**Chapter Three: - Venom**

Major Lorne and his security team had arrived, only a little too late. The snake had already come and gone, and the damage had been done.

Lorne saw Dr. Weir sitting on the floor against the wall and she was physically shaking as she clutched her bleeding arm. He wasted no time calling for a medical team before bending down to her level and carefully taking her right arm so he could take a closer look at the injury.

Surprised by his touch Elizabeth jumped a little when he tried to look at her arm.

"Easy Ma'am I just need to take a look at it." In doing so he could see the snakebite and it looked nasty, he could only guess how painful it must feel right now. His main concern was if the snakebite could be poisonous.

He felt the back of her hand to see if he could feel a change in temperature and gulped a little when he could. He double-checked by feeling her forehead and he got the same result; she was rather warm to the touch. It may well be just from the shock. But he wasn't taking any chances. Clicking his earpiece again he forwarded the information to Carson.

--

Carson was already on his way with a full support team when Major Lorne had contacted him. Activating his earpiece he returned the call. "Beckett."

"I need you to hurry Doc," came Major Lorne's voice. "I think the snakebite to Dr. Weir's arm might have been poisonous. She's running a high temperature and getting worse by the minute."

"Is she still awake lad?"

"Yes."

"Okay listen, I need you to keep her awake for me till I get there okay. Don't let her fall asleep."

"Would it be quicker if I came to you?"

"If you feel it's safe to move her. Then yes, we need to treat any poisonous symptoms ASAP."

"Will do Doc. Lorne out."

Carson started to double his pace and he ordered the rest of his team to do so. "Okay people lets move it."

--

John woke to the sound of wheels being rolled into the room. Opening his eyes, he turned to face the noise. He saw Elizabeth being wheeled in on a bed, which was parked next to his. "What's going on? What happened?"

Carson ordered various doses of medicine from a nurse and she hurried off to get them before he answered John's question. "We think the snake might have poisoned her."

John quickly got out of bed and went to stand by hers, ignoring the wires attached to him that were getting in the way. "It -was- one of those snakes we saw. How the hell did it happen?" It was then he noticed Lorne standing on the other side of her bed and looked at him. He could see his hands were covered in her blood. "We're supposed to stop this kind of thing from happening."

Carson looked at him before turning to see Major Lorne's guilty face before turning back to face him. "Don't blame him Colonel. The scanners didn't pick up the snake till it was too late." Carson gave Elizabeth some of the medicine the nurse had returned with.

Elizabeth had already passed out before they had got to the infirmary and Carson was concerned on how far the poison might have spread, if she was indeed infected. Quickly he pulled the scanner over and took a few quick readings.

It just confirmed what they were all afraid of and Carson's face said it all.

**TBC**


	4. Chapter 4: Worst is yet to come

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**Chapter Four:- Worst is yet to come**

Six hours had passed before Carson had given Dr. Weir the all clear. He had found an antidote and treated the infection straight away, by injecting it so it mixed with her blood to get rid of the poison. When Elizabeth came too, she had found not much progress had been made in capturing the creature from when she arrived in the infirmary.

The most annoying thing was that she was stuck with a sling rapped around her arm for the next week or so, since the snake and managed to break a bone in her forearm and it needed time to heal.

She couldn't remember much of her ordeal. Just that the creature was chasing her down corridor by the crew quarters and the next thing she knew was waking up in the infirmary.

John once again entered the infirmary. He'd been back and forth keeping her up to date with the information. Even though radio would have sufficed, he wanted the excuse to check up on her from time to time and not have Carson chuck him out the room for disturbing his patients.

Elizabeth pushed herself up into a seating position once he reached her bed and waited for whatever news was to follow.

John waved his arms about in frustration as he sat down in the visitor's chair. "Even with the improvements made to the computer systems from our last encounter with these snakes, it's still seems impossible for us to track the damn thing. At least before it showed up on sensors when it was ready to attack, now it's just random."

Elizabeth watched as the lights in the Infirmary began to flicker, guessing this place was going to be the next casualty in that department. "Don't suppose the power failure could be causing the sensors to malfunction?"

"It's plausible, McKay thought the same thing, but until we find the cause of the problem we won't know for certain?

Elizabeth rubbed her forehead when it started to ache a little and this got John concerned.

"You ok?"

She waved him off. "It's nothing. I'm fine."

"You don't look fine." John was about get Carson when Elizabeth grabbed his arm to stop him from getting out of his chair. Considering her fragile state her grip was pretty strong. "I'm fine honest. Just a mild headache that's all."

John wasn't convinced. "You should still get it checked out."

Carson must have heard the commotion for he was by her bedside in seconds. "Upsetting my patients again Colonel?"

John looked at Elizabeth to persuade her to tell him.

She sighed and looked at Carson. "I told John it's just a headache. I'm fine really."

Carson fished out his pen torch to double check his patients hypothesises and shone it at her eyes. "I'll be the judge of that."

Elizabeth found the light rather brighter then she would've expected and it must have shown for she didn't stop blinking. This got Carson to run a few other rudimentary checks whilst John sat watched with a worried look on his face.

"Pupils are slightly dilated and your body temperature seems to have dropped a little. Nothing uncommon, your body is probably experiencing the after effects of the shock to the system."

Carson went to his office, only to return with what looked like painkillers. "Take a couple of these and plenty of rest, you should fill much better by morning."

John nudged her arm playfully when he left. "See. You didn't have to suffer all that."

Reaching for the glass of water with her free hand, she later swallowed the tablets down in one go. "Trust me, I have suffered worse headaches."

"Why do you always push yourself to heard? It's not much of a walk from your office to the infirmary to grab a couple of painkillers when you need them or best off all you could always ask me to get them if needed."

Elizabeth slid down into her covers again in order to get some sleep. "Not now John. Must rest."

John sighed, if Elizabeth wasn't his boss and able to get out of conversations that easy he would've pushed harder. Instead he got up to leave, but he hadn't gone far when she called him back.

"Pass me another cover would you John. It's freezing in here."

John was sure something wasn't right, how could she be cold in the one blanket she had already and he didn't even have his jacket on. "Sure thing."

Elizabeth took it from him, and he help place it over her before leaving. He turned in time to see her snuggle up as tight as possible in order to keep warm.

**TBC**

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	5. Chapter 5: Darkness Unfolds

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**Chapter Five:- Darkness Unfolds**

Later that night, Elizabeth woke up to find the place extremely cold. She couldn't understand it; she already had two blankets and a bed cover on.

At first, when she opened her eyes, the place seemed to be in darkness. Once they had adjusted, her vision seemed out of focus to the movement, it felt like the whole room swam as though she was underwater. This made her fill a little sick and she quickly closed her eyes again for that feeling to go away.

She opened them again, only to find her vision was the same. Looking in the direction of Carson's office, she could see the light was on and quickly called for him. "Carson!"

Carson however had fallen asleep at his desk. After she called again, she decided to go to him herself and clambered out of bed, standing unsteadily on her feet. With each movement, she swayed here and there, grabbing whatever she could on the way to his office to steady herself.

She must have tripped on some wiring or something, for the next thing she knew, she was on the floor, the lights were now on, and a concerned Carson was immediately by her side checking her over.

He stopped her from getting up, so he could make sure she hadn't hurt herself in the fall. "You should've called me lass. Did you hurt yourself at all?"

Elizabeth winced a little when she tried to move, but couldn't feel anything broken. "No and I did call you Carson, twice."

Carson was about to help her up, but when she looked directly at him he almost did a double take when he saw the change in her eyes. "I can hazard a guess why you needed me."

He quickly lifted her right eyelid for a closer look. "This isn't good." Her eye had completely transformed to that of a reptile.

Elizabeth hated it when he didn't say what was wrong first before he started poking around.

This had her concerned. "What is it? What's wrong?"

Carson offered his hand and indicated the bed. "Let's get you back to bed first."

She winced a little when Carson helped her up and swayed the minute she was standing.

Carson steadied her quickly. "Whoa, easy lass."

As she clambered into bed she tried to find out what had Carson worried. "Is there something wrong with my eyes? My vision seems completely out of focus and I feel so cold."

Carson held up a finger and activated his earpiece to call someone, which turned out to be John. "Colonel Sheppard. You awake?"

--

John had taken a short break whilst the snake emergency had quietened a little; he had gotten tired of living off coffee for the past few days.

He stirred awake when he heard Carson's voice via his radio, which was sitting on his bedside unit. Without opening his eyes, for he was still half-asleep, he rummaged around with his left hand to search for his earpiece. Once he felt it, he picked it up and placed it in his ear then muffled his name. "Sheppard."

"_Colonel Sheppard. You awake enough to come to the Infirmary, we have a situation on our hands."_

John's eyes snapped open and he sat up fully alert. A knot quickly formed in his stomach knowing the call had something to do with Elizabeth. "I'll be right there."

--

"Carson. Tell me what's wrong?" asked Elizabeth again as he finished on his radio.

Carson pulled out a small mirror from his pocket and handed it to Elizabeth. She took it and looked at her reflection.

Shaking in fear at what she saw, her right hand reached up to the bottom of her left eye as she tried to come to terms with the change. To make sure she wasn't seeing things, she closed her eyes, only to open them again to the same view. "What's happening?"

Carson retrieved the mirror, when she sounded and looked scared. "I don't know love. I need to run some tests to find out."

It was at this stage that John came running into the room, and almost tripped over his feet when he saw the change in Elizabeth's eyes straight away since she immediately turned to face him. "What on earth?"

**TBC**

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	6. Chapter 6: Metamorphosis

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**Chapter Six:- Metamorphosis **

Ford, Teyla and Rodney had all gathered outside the Infirmary the minute they got word on Elizabeth's condition. So far an hour had passed and no news.

The lights flickering out in the corridor were driving Rodney crazy and he began walking up and down. "Surely he must know something by now."

As though he heard him, Carson arrived to see them and he quickly held up a hand before they could ask him how bad it was and intervened before they could all jump on him at once. "Dr. Weir appears to be undergoing some kind of metamorphosis due to the snake bite the other night."

"Is there a treatment for Dr. Weir's condition?"

Carson looked at Teyla and couldn't find an answer to her question, for he didn't know. "I wish I knew. I have tried numerous tests to counteract the change but none have been successful."

Rodney felt apprehensive about the next question, but it needed to be asked. "What is she changing into?"

"Most of the alteration appears to resemble that of the snake. But I think, if this is allowed to continue, she could be their next evolution in the developing world." O.o

Ford shivered at the thought of seeing Dr. Weir as a reptilian creature. "You said most of the alteration. Last we heard it was just her eyes? How much further has she progressed?"

Carson didn't want news to get out about this till he was certain there was nothing he could do. "I have promised Dr. Weir not to hand out the exact specifics, not yet."

"Please do not inform the base about this just yet. Now if you'll excuse me, I must get back to my patient." With that Carson turned and left, leaving the others a little stunned regarding the recent news.

--

Elizabeth was sleeping when Carson walked back in, and John was sitting by her bedside holding her reptilian hand, he looked up at him for a solution to this and new the Doc couldn't yet provide one.

"Would this change her personality Doc? If this progresses to the final stage?"

Carson sat down in the seat next to him. He wasn't surprised to see Dr. Weir sleeping, considering all the tests he had run. "I wish I new lad. I've never seen anything like this happen before."

John heard his radio activate and quickly responded to the message. "Sheppard."

"_Sir. The snake is back and is ransacking the science__lab. Dr. McKay and a squad of marines are heading their now."_

The message from the control room was distorted a little but John got the message clear enough. "Keep everyone away from that place. No one is to go near that snake. No one, you understand? I'll be at the lab shortly."

"_Yes. Sir."_

Carson could see John didn't want to go, but with Elizabeth incapacitated he was next in line to take command. "Go on. Go. I'll inform you if there is any development."

With Carson's assurance he didn't waste anytime getting down to the science lab. "Thanks Doc."

--

Upon arrival to the lab, John could see the room was a complete mess and he could only imagine Rodney's face when he saw this.

Waving his P-90 around as he entered further in, he searched every corner to see if the place was clear. He had asked everyone to stay clear; he didn't want anyone else affected by its bite.

John was about to turn to give the all clear, when suddenly an electrified tail lashed out from above.

**TBC**

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